


To Awaken Doubt in One

by blancanieve



Category: Star Trek Kelvin Universe, Star Trek: Alternate Original Series (Movies)
Genre: Angst, Emotional pain, Established Relationship, Fix It Fic, Hurt Bones, Jealousy and heartbreak, M/M, Minor Injuries, Misunderstandings, Oblivious Jim, Worried Jim, Yorktown setting, love and commitment
Language: English
Status: Completed
Published: 2017-11-24
Updated: 2017-12-02
Packaged: 2019-01-27 15:24:32
Rating: Not Rated
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 3
Words: 9,324
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/12584848
Author URL: https://archiveofourown.org/users/blancanieve/pseuds/blancanieve
Summary: Although they’ve been together since the Khan debacle, the way Jim acts with Spock causes Bones to have doubts about their relationship. When he finds out that Jim applied for the Yorktown Vice Admiral’s position, and Spock has also decided to leave the Enterprise, Leonard comes to a painful and devastating conclusion.





	1. Chapter 1

**Author's Note:**

> This story takes place on the Yorktown Base immediately after Bones and Spock rescue Jim in the drone ship.

 

 

**To Awaken Doubt in One**

**Chapter 1**

**“Though Earth and moon were gone,**  
**And suns and universes ceased to be,**  
**And Thou wert left alone,**  
**Every Existence would exist in Thee.”**  
**Emily Bronte**

Jim dangled from the life support hub of the Yorktown ventilation system, hanging on by the strength of his arms and sheer will power. Edison was gone, sucked out with the Abronath, but Jim was still hanging on. For a terrified split second, Bones glanced away from the ship’s controls to look up at him. It was all instinct this piloting of the drone ship. His skill and focus were all due to Jim, his insistence that Leonard become proficient in piloting all kinds of ships. “Your life or mine,” he'd grinned at Leonard, his blue eyes confident and shining, crinkling at the corners in the way Leonard loved, “might depend on it, Bones McCoy, so you _will_ do this.”

Sulu or Jim had taught him, drilled him and drilled him on all the ship’s shuttles and on every different sim available, until Leonard could pilot anything. Now Jim’s words had come to pass. He glanced up again and saw the desperation on Jim’s face; no fear, just desperation and the determination to hold on, knowing that the strength in his arms would give out sooner than later.

Leonard’s terrified heart was thudding loudly in his chest, but his hands were rock steady as he accelerated up. The small ship jerked under the G forces pulling at it, as he fought the controls to keep it steady. He accelerated up toward Jim, desperately trying to get closer to him. Spock half stood at the small opened ship hatch, and his long, strong Vulcan arms snaked up and grabbed Jim, as Leonard’s flying fingers held the damn ship still for the few seconds it took Spock to do it. Jim tumbled hard into the ship and lay sprawled on top of Spock.

“Spock, what would I do without you.” Leonard heard Jim say. And with that gasped comment, all of Leonard’s uncertainty and worry came rushing back. He hated himself for it, but for a long time now, he’d had doubts and questions. He’d lectured himself over and over again, told himself he was seeing thing that weren’t there. That, damn it, he was a grown man, not a teenager, so unsure of himself, that jealousy would rear its ugly head over every little thing. Then he’d found out that Jim had applied for the Vice Admiral’s position without telling him and that Spock was planning to leave the ship too. That had been the last bitter blow to his already shaken certainty. Somehow, he had to find the courage to talk to Jim about how he felt, how he'd felt for a long time.

Leonard had thought long and hard about how to tell Jim about his worry, his fears, his doubts. He was determined that he was not going to repeat the same mistakes he'd made with Jocelyn. Then his pain and fear had silenced him to the obvious deterioration of their marriage, avoiding what was plain to see. He knew he was not good at expressing his deepest emotions, but he also knew that this crippling inability had greatly contributed to the end of his marriage. But with Jim it had to be different, because Leonard loved the man beyond reason and good sense. When they were in bed together, entwined around each other, sated and blissful, Leonard’s heart felt as if it would burst with love for his Jim. After loving him for years, thinking his feelings were, and would always be unrequited, then discovering that Jim loved him too, their coming together had been all he'd hoped for, all he’d dreamed it would be.

He heard the two men behind him, grunting, trying to squeeze themselves into the tiny area behind him. He felt Jim’s warm hand squeeze his shoulder tightly in reassurance, but Leonard kept his eyes steadfastly on the horizon as he flew, still fearful that somehow he'd lose control of the tiny drone ship. He finally spotted the main Yorktown plaza and flew directly over it. He circled it, noticing that all Fleet personnel and civilians were gone, evacuated. He locked the landing gear in place and without a single tremor in his hands, piloted the ship down, landing it very carefully, gently. He turned off the engine, took a deep breath and slowly pried his clenched fingers from the navigation controls. Finally, thankfully, he pivoted in the seat to follow behind Jim and Spock as they carefully climbed out. Jim hobbled as he walked, obviously in pain, and Spock was bent almost double, clutching his wounded side.

Leonard, ignored his own bleeding forehead, to look carefully at the two injured men. “We all need to report to Medical immediately. Jim, you need treatment right away, you’re battered and bruised, probably have some broken ribs and that shoulder looks dislocated,” he said, visually checking him over carefully. It was a measure of Jim’s condition that he didn't even make a token protest. “Your wound also needs to be checked, Spock. I want to be sure it's healing properly and you need to get another dose of antimicrobials.”

Spock nodded. With Leonard on one side and Spock on the other, they herded the exhausted Jim gently toward the medical complex. However, at the Emergency entrance of the hospital, Leonard stopped short. He’d suddenly decided he wouldn't go in. Instead, he’d report to the Chief of Staff to tell him he was available to help with triage if they were short handed. Leonard knew there must be many injured Fleet personnel and civilians from the drones’ attack, and as a Starfleet doctor, it was his primary duty to offer help where and when he could. He gestured to Spock who nodded that he understood, and Leo turned away from the ER entrance toward the hospital’s main entrance.

Jim turned his head to see that Leonard was not walking beside them. ”Bones? Bones? Where are you going?” Jim’s bewildered voice followed him. “Bones, come back, you're bleeding! You need to go with us to the ER! Bones!”

Leonard could hear Spock’s soothing rumble explaining to the agitated Jim where he was going. He identified himself to the security officer who hurriedly directed him to the Chief of Staff. There he identified himself again to the clerk who immediately ushered him in to the CoS office. Recognizing him instantly, the startled Chief stood to greet him. He thanked Leo profusely for his offer. “But let's get that forehead abrasion taken care of first, Dr. McCoy.” He ushered Leonard into a treatment room where he personally cleaned and gently regenerated Leonard’s wound, all the while firmly assuring Leonard that they were fully staffed right now, but that yes, they would need him for the evening shift. It would be best, the CoS said, for Leonard to check in at Starfleet headquarters, get temporary housing and get some much needed rest before reporting for duty.

Taking his leave of the CoS, Leonard walked straight to the huge Starfleet complex located directly in front of the hospital. It was miraculously intact. Two burley red shirts saluted and directed him to the reception area. There he identified himself for the third time as the CMO of the _Enterprise_ , and explained his current plight. He asked the flustered clerks for temporary emergency billeting for the Captain and himself, also asked for two clean uniforms and for some ration bars. Finally, he was given his temporary housing security code, directions to the apartment, and the two sets of clothing along with a box filled with ration bars. With his arms full, he walked out the door. He stood there for a long moment mentally assessing himself. He was mostly all right, he decided. Miraculously and surprisingly, he had no major injuries, just bruises, protesting muscles, and the gash on his forehead which was now healed.

What he and Jim needed most was sleep. His exhausted brain and body informed him definitely and loudly that the two of them could do no more. As for everything else, as Scarlett O’Hara proclaimed in his favorite holo vid, they would think about it tomorrow. He sent Jim a short comm message telling him where they were billeted, and when Jim didn't respond, he walked to their temporary housing.

He hadn't even reached his quarters, when his comm began beeping frantically with an incoming call. Jim. “Bones, Bones, where are you? Are you alright? Bones answer me?” Jim sounded close to frantic.

“Jim, Jim, I'm fine. I'm just going to our temporary quarters. I've arranged everything, you just come find me when you're done. You need to rest, Jimmy, you’ve been through hell.” Leonard realized his own voice was hoarse and slurring with exhaustion, but there was nothing he could do about it. 

“Bones? You don't sound right. Where are you? Spock and I are finished at medical, we’re both fine. I'm coming to you in a few minutes.” Jim’s voice now sounded scared as well as frantic.

“I'm good, Jimmy, just very tired,” he responded, then gently closed his comm. Too exhausted to talk more, he opened the apartment door and walked in. Jim would come to him soon enough. He threw everything on the table in the living area before stepping into the sonic. He forced himself to do a five mnute cleanup in the sonic, then collapsed on the bed in his clean black briefs and t-shirt, groaning at the delicious feel of clean cool sheets. He closed his eyes, trying valiantly to stay awake to wait for Jim, but his eyes refused to stay open. His sheer exhaustion, his fright at almost losing Jim again, his trauma, his grief at the loss of their ship, of so many of their wonderful crew, finally and totally overwhelmed him. His eyes closed and he faded into sleep.

He woke suddenly, startled by the pounding on the door accompanied by a constant ringing of the door chime. A disoriented Leonard sat up, rubbed at his face and hair, then fumbled blindly around to find his pants. Not bothering with his blue shirt, he stumbled to the door and flung the door open.

“Jim!” He backed away from the door. “Come in. I was just trying to get a little rest and I fell asleep. Are you alright?”

Jim just looked at him. Worry and fright, all playing out on his mobile face, but it was Jim’s eyes that caught Leonard’s attention. They were blurry with a bone deep, weary fatigue and deep sorrow.

“I'm fine, Bones, all patched up. Are you alright? I got worried, because I couldn't find you at the hospital, then I had to go to headquarters to report to Commodore Paris.” He looked searchingly at the pale face in front of him. “Bones, you didn't even go with Spock and me to medical and you were bleeding! You scared me, Bonesy.”

Leonard breathed in deeply. “I'm sorry, Jim. I needed to go straight to the CoS to see if they needed medical help, and I just had to clear my head a little. Since you were with Spock, I knew you would be fine without me. Flying that drone really took it out of me. I'm a doctor, not a pilot,” he grumbled, heading back to the bed.

“Bones!” Jim put out a hand to stop him from moving away. He ran his hands gently over Leonard’s arms and torso, making sure he was unhurt, then leaned in to kiss him softly. “We’re alright, sweetheart, but we’re both completely exhausted so first we’ll rest, but after that you're going to tell me what's bothering you, because I know something is.”

Leonard opened his mouth, but Jim held up his hand. “Later, Bones. We’ll talk later. Let's go straight to bed.” He led Bones to the bed, sat him down, pulled off his pants, and pushed him gently down to the mattress. Then he pulled his own uniform off, also stripping to his briefs and t-shirt. “Sonic, later,” he muttered exhaustedly. He scooted in next to Bones’ warm body, turned to him, pulled him gently into his arms, and gripped him tightly. Leonard went willingly. He was very tired, but so blissed out at actually having Jim here, alive and well, that he wondered how he had even managed while being away from him.

“Sleep, baby. Let's go to sleep. Lights 10 percent,” Jim commanded the computer, and Leonard closed his eyes.

They woke as they so often did, at exactly the same time. Leonard felt Jim’s hard-on pressing against his thigh. No matter the circumstances, Jim’s libido was as sure as death and taxes, he thought lovingly, and turned to face his oh so predictable Jim. Leonard craved these lovemaking sessions with Jim. First, because during sex his doubts and worry were silenced, and secondly, because their lovemaking was, and had always been, mutually passionate and deeply satisfying. Heated blue eyes met equally heated hazel ones and Jim moved in quickly to lick across Bones’ lips. He dove in greedily, opening Bones’ mouth with his tongue and heat flared instantly in Leonard’s belly. Jim rocked against him rutting together. They were still in their black briefs, but they hurriedly pulled them off. Leonard bit at Jim’s bottom lip, then soothed the bite with his tongue. Jim groaned and Leonard realized how badly, desperately, his body and soul needed this, to feel all of Jim’s naked skin, to hear Jim moaning and passionately aroused against him. Jim’s hands raked up and down Leonard’s chest and Leonard moaned pressing their hips harder together, sucking on Jim’s bottom lip.

“Bones, Bones, Bones,” Jim chanted. In the dim light, Leonard could see that his cheeks were flushed, his bottom lip bitten red. Jim wrapped his fingers around Leonard’s cock and Leonard pushed desperately up into Jim’s fist and groaned at the feel of those hot, curled fingers around him.

“Jim, Jim, you feel so good, so good.”

Jim dug his nails into Leonard’s back, his tight grasp becoming almost frantic. His hand began to stroke Leonard in earnest, and he twisted his wrist just so, until Leonard growled at the feel of it. He could hear the thrum of his own rapid pulse drumming in his ears.  

“Bones,” Jim said breathlessly, “make that sound again.”

Leonard did, and Jim moaned in response. “Again, Bones, let me hear you again,” he whispered. “Bones…Bones…love you like this, so hot, so gorgeous, just for me, baby,” he murmured. Jim spread Leonard’s thighs wide, his right hand moving to stroke Bones and his left hand rubbing slow circles into Bones’ sensitive flesh between his legs.  
   
Leonard groaned again as his orgasm caught him by surprise. It was sudden, hot and intense, rushing through his chest, his arms, his belly, burning him with the heat of it. Jim continued stroking him, keeping his orgasm going, going, going, until, at last, Leonard lay spent and sated beside him. With the power and strength of his orgasm, the buzzing anxiety and terror in his head finally stopped and the reality of Jim alive, grimy, hot and sweaty beside him finally became a blessed reality.

“Jim,” he murmured, as Jim rutted desperately against Leonard. Leonard bit at Jim’s lips, tasting  iron, stardust, and home in Jim’s mouth. Jim gasped, writhing against Leonard’s hand, until he shuddered and came, his cum spurting thick and hot against Leonard’s stomach.

“There you go, darlin,” Leonard murmured into his mouth, as Jim finally came down from his intense climax and settled warm and sated beside him. He reached for one of their discarded briefs and wiped them both down.

Jim sighed deeply, stroking Leonard’s face with gentle fingers. “I was so scared, Bones,” he murmured. “The only thing that kept me going was the fact that you were with Spock. I knew he'd do his best to keep you safe for me. I had no idea he was wounded, and you were the one taking care of him. My Bones, so brave. He told me you saved his life.” Jim kissed him tenderly and intertwined their fingers together,

“I was scared shitless, Jim. I thought he was goin’ to die, and I didn't even have a med kit with me.” He shuddered. “I did all I could with what I had, and I saved your best friend for you.”

“Bones! What are you talking about? You're my best friend, always have been, always will be.”

Leonard sighed, his hazel eyes troubled and filled with doubt as they looked into the blue eyes he adored. “Really, Jim?” He ran his hand gently over Jim’s stubbled face. “I’ve been wondering about that for a while now.”

“Bones!” Jim looked stunned. “You've always been my best friend, from the moment we met on that shuttle.” He raised his torso off the bed and pillowed his head on his hand, his brilliant blue eyes looking intently at Leonard, his other hand still entwined around Bones’. “Is this what's been bothering you, Bonesy? I’ve known for a while something was, but it seemed you weren’t ready to tell me and I didn’t want to push you.”

Leonard shifted his eyes away from the intensity of the question in Jim’s eyes.

“Bones, please look at me, tell me what the hell you’ve been thinking, what’s been going round that head of yours about Spock that’s been worrying you so?” Jim looked at him in such bewilderment, that Leonard felt himself crumbling. Finally, he would tell Jim about his worry, his doubts, and even, shamefully, about his jealousy. He knew this was a terrible time to do this, after all the horror, trauma, and pain they'd just been through, but Jim looked worried and he was asking so it seemed he really wanted to know, and Leonard couldn't hold it in any longer. The silence squeezing his throat and keeping his secret had become unbearable, his fear eating at him from the inside out.

Leonard sighed shakily, finding it hard to meet Jim’s eyes as he spoke. “Alright, Jimmy. I know this isn’t really the right time after what we’ve all been through.”  He shuddered, “and after I almost lost you again, but I've kept it inside of me for far too long. I should have talked to you about this a long time ago, but I was too scared.”  Finally, he met Jim’s patient, gentle and puzzled gaze. Leonard cleared his suddenly constricted throat. “For three long years, all the way back to when this mission started and even before then when we were just friends, I've watched you turn yourself inside out and upside down for Spock, and I've driven myself crazy watching you do it.”

Jim’s eyes opened wide and he opened his mouth to protest, but Leonard put a gentle finger against his lips. “Please, Jim. Let me finish because this is so damn hard, that I can only do it once.” He would get this all out even if it killed him. Jim nodded, biting his lip. The words began pouring out of Leonard. “I get that you wanted to be friends with Spock, I do, like you saw in that mind meld with old Spock. But this thing with you and our Spock, it's always seemed so much more than that to me. From the very beginnin’, I couldn't understand it, especially after the way Spock treated you, accussing you of cheating on the Kobayashi Maru, humiliating you in front of the Admirals, in front of the entire Academy, then getting you grounded. All of it because of him, Jim, and if it hadn't been that I sneaked you on board the ship, we’d all be dead.”

Jim clutched him tightly. “Bones….”

Leonard ignored his whispered protest. “Then after we got on the ship, Spock wouldn't even listen to you, instead he dumped your ass on Delta Vega and then nearly choked you to death! But in spite of all he did to you, you still got the _Enterprise._ You still became Captain, and I was so proud of you, Jim, so proud to be the first one to sign on with you. You worked real hard to get all the crew you wanted, but I could tell you weren't really satisfied until you got Spock. Then, once he was your XO, I saw how you tried to win him over, the smiles you’d give him every time he did somethin’ you liked, your invitations to play chess, to eat with you. I saw it all. I also saw how mostly he just ignored you, but you kept on tryin’, even though he still acted like a total dick to you.”

“Then after the shit storm of Nibiru when you saved his life? What did the bastard do? He reported you to the Admiralty for breaking the prime directive and for lying on your report. And thanks to him they took away your ship and your Command. But you? You still asked him to go with you to get Khan. And after Khan, when you were dying in the warp core? You didn't ask for me, Jim. It  was to Spock that you gave your last moments. Your last words were for him, not for me.” The hitch in Bones’ breath betrayed his grief as he remembered. “It was Spock who comforted you through that glass as you died, and that, Jim? That hurt me most of all.”

Leonard finally turned to face him, and at the raw pain he saw on Bones’ face something twisted in Jim’s chest. At the sound of Jim’s indrawn breath, Bones huffed a bitter, hoarse laugh. “Yeah, Spock told me. He came to the Med Bay afterward and told me about those last moments you shared with him, how you were afraid, how he lost his cool watching you die. And Me? Your best friend? All I got was you in that body bag.” Leonard shuddered and he clutched Jim tightly as he remembered his utter devastation, the overwhelming feeling of horror and loss at seeing Jim in that body bag. Jim, his beautiful Jim, dead.

Leonard’s jaw muscles bunched at the memory and he blinked hard. “And you know what, Jim? When I saw you there dead, I think I went a little crazy. I became like a Dr. Frankenstein, trying to bring you back from the dead. It scares me, you know,” he murmured, his eyes glassy with the memory of his anguish, “what I’m willing to do for you, all because I can’t stand to live in a world without you in it. I didn't eat or sleep. I survived on stims, and I stayed right by your side the whole time.” Leonard’s voice broke and he drew in a steadying breath. “Then you woke up and you only thanked Spock for saving your life. Even if I didn’t show it, that hurt me real bad, Jim,” Leonard whispered and closed his eyes in remembered pain.

“Bones…Bones…don't, don’t. I’m sorry, so sorry, I totally screwed up, I know I did,” Jim whispered and ran his warm hands up and down Bones’ arms trying to comfort him.

Leonard grasped one of Jim’s hands and held on tightly. “But then when you got better, when you told me you loved me, when we got together, really together, it was like a miracle to me. I was so happy, Jim, so happy, because I had loved you for so long. I put away all my hurt and jealousy, because being with you was everything I dreamed it would be. And you seemed happy too, happy being with me, happy in our bed, happy with lovin’ me.”

“Bones…,” Jim whispered, utterly devastated by the anguished words he was hearing. “I was! I am!”

Leonard pivoted away from Jim’s warm arms, turned on his back and looked up at the ceiling. “I even talked to Nyota about it, because even though you and me were together and she and Spock were too, I still saw you doing all that same stuff with Spock.” He sighed. “She didn't like it neither, but we both agreed we’d just try to ignore it, because every day it was to me that you came home to, and Spock went home to Ny.”

The bed creaked as Leonard shifted restlessly. Every bone and muscle in his body hurt. “But then I found out you put in for the Vice Admiral’s job here on Yorktown. You did it without sayin’ a word to me, Jim. I know Uhura told you that she and Spock had broken up. She was so heartbroken he was leaving that she came to talk to me. That’s when she mentioned you'd sent the application in her data packet. Of course she thought I already knew.” Leonard sighed wearily. “I waited for you to tell me, to explain, but you didn't, so I figured you just didn't wanna’ stay on as Captain without Spock being by your side. Since you didn’t talk to me about it, I didn't even know if you were gonna’ leave me behind when you accepted the job. So I finally got brave enough to talk to you about it because I had to know how you felt, but that was the day when all hell broke loose with the drone ships and Krall.” He turned to look at Jim, his face deathly pale and infinitely weary. “I just want you to know that in spite of how I felt, I did the best I could on Altamid to take care of Spock for you.”

Jim hand came to rest on Bones’ chest where he could feel his heart thudding frantically in his agitation. ”Bones, Bones, you should have told me all this before, told me how you felt all this time.”

Bones went on as if he hadn't heard Jim. “And today? It was me who got Spock and me on that drone ship. It was me who flew us where you and Krall were fighting. It was me who flew the drone ship up under you so Spock could pull you in. It was me who fixed up Spock’s wound so he was strong enough to grab hold of you. But the first words out of your mouth were ‘Spock, what would I do without you.’ It was like I wasn’t even there, Jim, like I didn't even count, like I hadn't done a damn thing.”

Bones closed his eyes tightly. He was so very tired and this conversation with Jim was killing him, but he went on. “So now I have to ask you, Jim, ask you to tell me the truth ‘cause I have to know. Is it Spock that you always wanted? Was I your fall back guy, your second choice, because Spock was already with Ny?”


	2. Chapter 2

**To Waken Doubt in One**

**Chapter 2**

**“Just like there's always time for pain,**  
**there's always time for healing.”**  
**Jennifer Brown**

 

“Bones, no…no…!” Jim’s’ face was a mask of shock as he faced Bones. His heart felt shattered at the words he'd just heard. How was it possible that he’d been so oblivious, so wrapped up in his command responsibilities that all this time he’d been blind to Bones’ doubts, his pain? During their private time together, in their quarters, on shore leave, during lovemaking, how had Jim not noticed that Bones was hiding this terrible hurt from him?

Leonard ignored Jim’s distraught, whispered words. “I tried Jim, I tried real hard to close my eyes to it, to ignore how you were with Spock, because I was dreadin’ that you'd tell me what I feared was true, that it was Spock that you really wanted, and that I'd lose you. Sometimes, when things between us were so good, I’d be able to push the whole thing to the back of my mind for a while, but then I’d see somethin’ between the two of you, and it would all come rushin’ back.” He rubbed his hand down his stubbled face wearily. “I know I was a coward, Jimmy, not tellin’ you. I’m ashamed of that…but it's because I love you so damn much. I always have. Losing you has always been my greatest fear. I'd do anything for you, which I guess you already know, after what I did with Khan’s blood. I broke my oaths, Jim, I threw everything I held sacred as a doctor out the window, and I didn’t even think twice ‘bout doin’ it.”

“Bones…Bones….no.” Jim told him again, his voice broken and hoarse. He stared wide eyed at Bones, feeling dizzy and lightheaded, his heart hammering uncomfortably in his chest. He felt sick at the knowledge that Bones’ had lived with these doubts, this uncertainty for so long, that he’d been so unsure of Jim’s love for him.

Leonard turned on his side so he was face to face with Jim again, his hazel eyes dark. “I just want you to tell me the truth, Jim, ‘cause this isn’t gonna’ be like it was with Jocelyn, me loving someone so much and not being loved back, me being left behind because there was someone else. I can't go through that hell again. You were a witness to what it did to me. It almost destroyed me. So no matter what, I rather hear the truth from you, I _need_ to hear the truth. If it’s true, you won't have to worry ‘bout me. If Spock’s who you want, I’ll learn to live with it somehow, at least until our mission is over. I won't get in your way or make any kind of fuss. I can be professional, both in the Med Bay and on the bridge. Or if you and Spock want another CMO, I can ask Dr. Boyce for a transfer and go somewhere else, to another ship, or to some planet somewhere. He’ll do it for me if I ask him.”

There were shadows of deep pain in his eyes, but Leonard looked at the terrified Jim steadily, resolutely. “I’m just so damn tired of thinkin’ about it all, worrying about you and Spock, wondering if you’re gonna’ leave me. I just want you to be happy,  Jim, ‘cause you, of all people, deserve to be happy, even if it’s not with me. So if Spock is who you really want, you just have to tell me and you can have your chance with him, unless he and Ny are gettin’ back together, but maybe if you work real fast you can beat her to the punch.”

Bones took a deep shaky breath and Jim saw his eyes, those beautiful pools of swirling colors that Jim loved so much, suddenly brighten with unshed tears. Bones raised his free hand to squeeze the bridge of his nose as he swallowed hard, trying to get control of his emotions. Jim looked at the white, exhausted face, at the heartbroken, beautiful eyes, and, unbidden, an old, bitter saying of his Grandfather Tiberius came to mind; “None are so blind as they who will not see.”

He clutched tightly at Bones’ t-shirted arm to ground himself, as his mind went racing back to all their years together. Memories. So many memories flashed through his mind. He thought of the Maru, of Delta Vega, what he had done to Spock to get command. He thought about Nero and _The Vengeance_. He thought about Khan and Bones’ arm stuck in the torpedo, about Marcus and the Augments and how close his entire crew had come to death. He thought about the warp core, about Death’s cold hands finally claiming him, about Bones bringing him back from the dead. He thought about Krall, of his twisted plans for revenge. He thought of his single minded focus during each of those terrible events, of what he had done to accomplish what he felt he had to do. And finally, Jim thought of the magnitude of what he might have lost because of his actions. Nero’s destruction of the Med Bay while Bones was stuck in the lift, Bones’ narrow escape from the torpedo, Bones and his entire crew almost being annihilated by Marcus and Khan, Bones barely escaping being court martialed and thrown into a military prison because of his serum, Bones on Altamid, standing utterly alone, surrounded by the drone ships, about to be killed, before Scotty beamed him out.

Jim gathered his scattered wits and found his voice, grasping Bones’ frantically. “Bones, no! No baby! No, no, no! It's not like that. I promise you.” He groaned aloud. Stupid, he was so damn stupid! So incredibly blind and stupid! He prayed that somehow he could make this right, make Bones see how much Jim loved him. “It’s true that I didn't talk to you about Yorktown, but only because I changed my mind about the application and recalled it, even though Admiral Paris told me that the job was mine if I wanted it. It was just a dumb impulsive thing that I did because I was feeling fed up with the way our 5 year mission was going. I know I should’ve talked to you about how I was feeling, Bones, but I was so ashamed that I wasn’t handling things well by myself. I’m the Captain, I should be able to keep it together. I felt worn down, worried all the time about the crew, about the ship, about the 5 year mission, and I didn’t want to worry you too.”

Jim cupped Bones’ face between trembling hands and stared deeply into the hazel eyes. “Both of us were idiots, Bones, hiding our feelings from each other, but you listen to me, Bones McCoy, I would never go anywhere without you. I would never leave you behind, never! I couldn’t do it. It would kill me! And I promise you, it had absolutely nothing to do with Spock’s decision to leave the ship. He hadn't even told me he was thinking of leaving. All I knew was what Ny told me, that they were breaking up.”

Bones looked back at him, doubt written all over his face. Jim seeing that doubt whispered, “I'm sorry, so damn sorry. God! You're everything to me, Bones, everything, and I should have told you that every damn day of my life.”

Jim swallowed hard remembering the horror of his warp core climb, his fall, his death from the painful, burning, lethal radiation. It was something he never looked back at too closely, because the memory of it terrified him. “I know we should have talked about my dying long ago, but it was just too hard, too damn painful for both of us to talk about, but I want you to know that I didn't call for Spock when I was dying. I didn't, Bones. Scotty did. Suddenly Spock was just there on the other side of the glass, finally trying to be the friend he hadn't been before and a comfort to me, as best he could. But I wanted you, Bones; I wanted you so terribly, but I knew if you came you'd try to open that door to get to me. In my head I kept calling for you, but I couldn't let that happen to you, love. If you had died too it would all have been for nothing.”

Jim bit down hard on his lip, tasting blood. “This is all on me, Bones. All of it. I should've told you how I deeply I feel about you, but I've always been shit about expressing my deepest feelings, they're too strong, too overwhelming, the right words don’t come, and I’m always afraid I'll be too much, that you'll get sick of me or that you’ll think I’m crazy and I'll scare you off.”

Jim wiggled closer to Bones’ warmth, giving him frantic, hard little kisses all over his face. “You are the single most important person in my life; it's been that way since the day we met on that shuttle. I lost my heart to you on that shuttle ride and I’ve never gotten it back. Through all my shit, my successes, my failures, you've loved and accepted me, you've healed me innumerable times. You’re the only person, the only one, Bones, that I’ve ever loved. You belong to me and I belong to you. God! I love you so much. When you're around me, I want to touch you all the time, I can hardly keep my hands off you. I covet even those small moments when I catch a glimpse of you on the ship. When you come up to the bridge to see me it satisfies something in me, it makes my whole day better. Why do you think I go down to the Med Bay all the damn time? I need to see you, that’s why. You don't know, Bones, sometimes I want you so much, I make myself sick with it. No matter how often we make love, it's never enough.”

Jim shook his head helplessly and cleared his suddenly clogged throat, looking steadfastly at Bones. “You're the only person who’s stayed by my side, never left me behind; you've been my friend, my confidant, my lover, the other half of my soul. You  made me a whole person when I was broken. You brought me back from the dead! You fought death for me and you won. No one else could have done what you did! No one else would have even dared. I'm only here because of you,” Jim said, his voice broken. “I've seen into your soul, into the huge heart of yours, Leonard McCoy.” Jim rested his forehead against Bones’. “I know how good and true you are, how much you love me. Please, Bones, give me another chance to prove to you how much you mean to me, how much I do love you. You can be angry with me, disappointed in me, but please, please give me another chance.”

In his heart and soul, Jim knew he wouldn't be able to live without seeing Bones’ beautiful eyes every day, or the man they belonged to. “How can I prove it to you, baby? Just tell me how and I’ll do it, whatever it takes, I’ll do it. It's you and me, Bones. Nothing and no one else matters to me like you do. I don't want Spock, I don’t. All I wanted was for him and me to become that unstoppable command team I saw in that mind meld that's it. You know how I can be when I set my mind to something. I just got caught up with what Old Spock told me about Spock and me being great friends and becoming a legendary command team.” He drew in a deep shaky breath. “That's all it was, Bones, that's all it ever was.”

 _Yes_ , he thought bitterly, _and the evidence of your stubborn, single minded focus to win Spock over is in front of you, broken hearted._ Jim had always believed there was a special place in hell for anyone who hurt Leonard McCoy, and to discover that he was the one who’d hurt Bones eviscerated him completely. Jim shook his head impatiently. Right now he had to swallow his own pain to concentrate on Bones. “I just thought too damn much about how to make it happen. I got obsessed with trying to prove to everybody, to the Admirals, to the other Captains, to my crew, to myself, that we could be the best command team in all of Starfleet. I needed to prove that I wasn't that hick farm boy from Iowa that only got into the Academy because of Pike, because of being George Kirk’s son, that I only got to be Captain because of Nero and blind luck.”

Jim hugged Bones closer, and folded him into his hungry arms, cradling him like he’d never let him go. Jim’s hands began to move, to stroke Bones’ shoulders, his chest, his neck, his back, trying to touch everywhere at once. “Bones,” he whispered shakily, brushing the thick dark hair back from his forehead. Jim wrapped his arms tightly around Bones’ stiff body, feeling the racing pulse in Bones’ throat, the frantic heart beat pressed so tightly against Jim. Then Jim buried his head in the crook of Leonard's neck, desperately breathing in the scent of this man he couldn't live without.

.


	3. Chapter 3

**To Waken Doubts in One**

**Chapter 3**

**“Just like there's always time for pain,  
there's always time for healing.”  
Jennifer Brown,**

 

Jim made a wounded noise in his throat. “Listen to me, please, Bones. I wouldn't have made it without you," Jim murmured thickly. “I wouldn't have made it through the Academy, or Nero, or Khan, or Krall, without you.” He carded his trembling fingers up through the thick dark hair and pressed a gentle kiss to his temple, holding his lips against the soft skin there for a long moment. “Oh, Bones,” Jim breathed softly in his ear, “please believe me, I love you so much, so much, sweetheart. You're the best man I know. I fell in love with you when you looked at me on that shuttle, when you cared about me from that very first day. It's always been you, Bones. Always. You and me, that’s all I’ve got in this universe, just you and me.” And Jim, who always prided himself on his silver tongue, on his ability to talk his way around and through anything, was suddenly and completely bereft of words.

Leonard shuddered and a shaky breath escaped him. His arms finally came around Jim, and in the hazel gaze looking searchingly at him, Jim could see a myriad flash of emotions swirling there. There was love and hope in those eyes, but doubt too. “But why, Jim? Why did you act that way…with...Spock? If you’d just told me why you were doing it, I would’ve understood. I’m a grown man, not some delicate flower who can't handle the truth.” He sighed. “I watched you, watched what you’d do, and Jesus, Jim, you have no idea what it did to me. I tried to accept it, to not be jealous, to understand that Spock must give you something that you needed that I just can’t seem to...no matter how much I tried,” he added sadly.

Jim shook his head and swallowed hard. He rubbed hard at his chest feeling an actual ache there, realizing how much he’d hurt Bones. “No, love. You’ve always given me everything I need and much more besides. Spock is my friend now, my brilliant First Officer, but he can go to hell if my being around him hurts you like this. There's no possible excuse for my making you feel this way, absolutely none. But,” he added softly, knowing he had to somehow make Bones understand, “maybe I can explain it to you, just a little, why I’ve been such an oblivious, blind fool.”

Jim sat up and leaned his back against the headboard, pulling gently at Bones. “C’mere, Bonesy, so I can tell you.” He kept his arms around Bones as he sat up, his hands sliding around Bones, afraid to let him go, the weight of his warm body grounding him, assuring himself that Bones was still with him. Jim stroked him gently, running a soothing warm hand up and down his arm and back. “You’re everything to me, Bones. From the beginning, you've always been everything. Immutable, unchanging, the very bedrock of my existence, like the earth below my feet, the stars above me.” He paused thinking how to say the right words to express his truth about Bones. “What I’m telling you isn't an excuse, it's not, but I don't really think about those things. They just **_are,_** a part of my existence, of my life. It's the same way with you. You’re like the air I breathe, like the universe around me. There’s nothing without you, not one damn thing.” Jim put his forehead against Bones’ temple. “But, I promise you, love, that never again will anything I say or do make you feel like you're not the most important person in the world to me. I can’t live without you, Bones. I can't,” he whispered. “Please, please, say you’ll forgive me and let me make it up to you. Please, Bones, I'm begging you.”

“Jesus, Jim.”  Bones whispered. “Don't. Don't, darlin’. You don't ever have to beg me. You know I can’t ever refuse you anythin’. But…but...if you're really telling me that things will be different, I will. Of course I will. I’ll forgive you.”

“I am telling you, Bones, and I promise you with my whole heart that things will be different.” Jim’s whole body shivered in a surge of wild relief, but he was still unsure, uncertain. His heart beat anxiously, thudding against his chest, knowing how much damage and pain he'd caused. He blurted out, “Please, Bones, I gotta’ know. I haven't ruined everything between us, have I? Please, please tell me that you still love me. Still love me the way you always have.”

“Jim! Of course I still love you,” Bones answered, his hazel eyes fierce. “I always will, you single minded, crazy,  beautiful man. I cain’t seem to help myself, I love you so goddamn much,” Bones said in that deep, soft, southern drawl that only appeared when he was feeling very stressed or very passionate. “Seems like nothin’ can destroy how I feel about you. I think I just love you too damn much.” He said it like a confession, the gold, green and amber in his eyes swirling with emotions he couldn't articulate.

Jim kissed him then, kissed him deeply, pouring every ounce of his love into the kiss, and like always, it was like the very first time he’d ever kissed Bones. His lips were soft, enticing, addictive. Jim had always been greedy for that mouth, those kisses.

“It's alright, Bones, it's alright to love me too damn much, because I love you the exactly the same way. You’re _mine, mine,”_ Jim whispered the words over and over into Bones’ skin, against his beautiful mouth, his touch almost frantic. Because of his blindness, his complacency in taking this brilliant, loving man for granted, he’d hurt his Bones, almost destroyed what they had built between them, the friendship, the trust, the love. Jim kept murmuring words of comfort, of reassurance, until at last, Bones’ stiff, tense body began to respond to Jim’s murmured endearments and he slowly relaxed in his arms.

When Bones' hand came up to wrap warm and strong around the back of Jim's neck, stroking the short hair there, and when he finally whispered, “I love you,” Jim’s fears finally began to ease as he heard the love in that soft whisper. He scooted closer, pressing himself against the warmth of Bones’ body as he kissed him again, and this time the kiss was intense, hard, almost brutal, not careful or hesitant as Jim poured all his feelings into it. The passion between them, always simmering beneath the surface, blazed to life instantly and Jim’s tongue was probing, exploring, pushing inside like a starving man seeking nourishment. Bones kissed back responding with the same urgency, his lips answering Jim with the reassurance, the affirmation, that he was still wanted, that Jim was still his just as much as he was Jim's.

He could never get enough of this, Jim thought dazedly. Bones’ lips were sinful, tasting wonderfully familiar. Jim’s hands traveled up and down feeling the taut muscles, the warm, perfect, silky skin of Bones’ back. From their first time falling into bed together, it had always been like this. Bones drove him crazy every single time he wrapped himself around Jim, the taste of him, the feel of him, the scent that was so uniquely his.

“I love you so much,” Jim breathed against him. "You haven't heard that nearly enough from me. Want you, Bones, aways, always want you. You’re all I’ve ever wanted. I’ve loved you for so long it feels like I was born loving you. I'm so sorry I hurt you. Don’t ever leave me, Bones,” Jim told him simply. “I couldn't live if you did.”

Bones’ eyelashes fluttered at those words, and his eyes closed, his body suddenly going soft, pliant in Jim’s arms. The unbearable tension he’d felt for so long, finally giving way to profound relief at hearing Jim’s words. Bones opened his eyes and in their hazel depths, Jim could see the love, the devotion Bones felt for him. He pressed his forehead against Jim’s. “I wouldn’t, Jim, I couldn’t. Where the hell would I go?” He asked, his voice raspy with emotion. “I can barely walk and talk without you, haven’t been able to for years?”

Jim smiled exhaustedly and dopily at him, his blue eyes shining with his deep, vast, relief. “I'm going to make it up to you, Bonsey,” he crooned softly. “You’ll see. I’m going all the way back to ‘I might throw up on you,’ from the moment when I fell in love with you. I will, I promise. I’ll make it up to you for all the times I’ve made you sad, made you doubt how much I love you." Jim knew he was babbling, but he couldn't seem to help it, his relief was so great, so all encompassing that he felt giddy with it.

Leonard huffed as he drew in a deep, shaky breath. “No need to go crazy, Jim Kirk, or go back through all the years of our past history. I believe you. But if I ever see you making goo goo eyes at Spock again, that’s it. He's going right out the airlock and you after him,” he groused, summoning up some small shred of his usual testiness. “I've had it with all that shit, and,” he added as an afterthought, “I'm sure Ny has too, and I bet she's also gonna’ tell Spock exactly how the cow ate the cabbage about that very thing.”

Jim chuckled with delight, something tight inside of him loosening at hearing the faint return of Bones’ southern colloquialisms and grumbling, but his grip on Bones remained tight and possessive. Jim’s world had wobbled dangerously, precariously, hearing all that Bones had told him, but it was tilting back on its axis. Jim had never really believed in fate or destiny, but it seemed to him that the universe had always conspired to keep him and Bones together. Somehow, it came down to them always being _JimandBones._ He knew he still had a lot of work to do to erase the pain and doubt he'd caused, but he would do whatever it took to assure Bones that he was profoundly loved. For now, Jim kept on murmuring words of comfort and reassurance in Bones’ ear, beginning as he meant to go. 

“Feeling better, baby?" he asked Bones softly.

Leonard nuzzled into his neck and sighed. "In every way possible," he answered. “I’ve been so scared for so long that I was losing you to Spock.”

“Never!” Jim held him even closer, their bodies almost fused together. This wasn’t about the endless passion Jim always felt for Bones, or about the fantastic sex they’d always shared, or about the deep friendship and bond they'd forged since their Academy days, or even about the fact that his life wasn't worth shit without Bones in it. This was about how Jim was going to live the rest of his life with Bones right at his side, both now and later, when they were through with Starfleet. It was about love and forgiveness, it was about cherishing and taking care of his doctor like he’d always taken care of Jim, it was about making sure Bones knew how amazing he was, how deeply he was loved and needed.

When he was a child, Jim had slowly and painfully acquired the knowledge that life was messy, difficult and complicated, that love was hard won, that it made you terribly vulnerable, that sometimes it broke your heart and that there really was no such thing as a happily ever after. But here and now, Jim vowed to himself that from this day on, he was going to cherish his doctor, guarding his heart and keeping it as safe as was humanly possible. He was going to try for that happily ever after because Bones deserved nothing less.

Jim yawned; a profound deep bone tiredness suddenly overwhelming him. It was the cumulative fatigue from his battle with Krall and his drones, from the profound sorrow at the loss of his crew and his ship, and from the fear and emotional upheaval at the thought of losing Bones. It was all finally crashing down on him hard. “What do you say we go back to sleep for a little while more, Bonsey. We’re both still exhausted. When we wake up we’ll comm Joanna, Sam, and our moms. They probably haven't heard the news about Krall yet. We’ll save them a lot of worry if they hear it from us first before Fleet notifies them or it hits the news nets.”

He sighed, softly, sorrowfully. “We should rest while we can, Bones. We’ll have a lot to do when we wake up.” Jim said it mournfully, the light in his usually bright blue eyes dimmed with sadness. Jim knew that neither of them had really absorbed the full magnitude of what had happened, that the next time they woke they'd have to confront the reality of their situation; his beautiful ship, the ship Chris Pike had entrusted to him destroyed, lying broken, torn apart on Altamid, so many of their wonderful crew injured or killed, the survivors traumatized and scattered all over Yorktown. They would have to deal with all of that, but, particularly for Jim as Captain, it was a profoundly painful, bitter, and devastating loss.

Leonard knew that very soon Jim would have to put on the mantle of Captain, setting aside his own pain and sorrow, in order to be a strong leader for his devastated crew. He would have very little time for mourning all that he had lost. Leonard would have to keep a very close eye on him, on all the crew, and ironically, someone else would have to keep a close eye on him. Physician heal thyself wouldn’t work this time around.

“Spock told me he'd begin scanning for the remaining crew’s bio signs so we can locate them all. He told me he was going to ask Uhura to help him.”

Len nodded against Jim’s jaw. A good sign that. Maybe Spock had come to his senses after all.

“We need to gather the remaining crew together, find housing for them, and have medical treat them, both physically and mentally. Being together is what we all need, finding some comfort and healing in each other. But I'm supposed to get some rest first, ‘For as you know, Captain, Vulcans have a much higher degree of physical stamina than do humans,’ he intoned to Bones in an uncanny imitation of Spock.

Bones snorted and Jim smiled slightly, although his heart was heavy with grief.  He felt battered and bruised with sorrow. but with Bones beside him, they could and would somehow overcome what had happened to them at the hands of yet another madman. They would share their grief and their sadness, holding each other close to make it bearable. They would somehow endure and go on together; always together, just as they had always done.


End file.
